Best: Probably Majora (all three forms) because you could beat him in so many different ways, which gave that battle some good replay value (now as I think of it: Is it possible to go through the whole battle with Deku Link only? If yes then that'd be the ultimate challenge!)
Others on the top of my list: aLttP Ganon, OoT Phantom Ganon, Twinrova, Koloktos
Worst: I guess Gohma in most of her incarnations. In LoZ a simple arrow into the eye, quickly shot when entering the boss room ends the battle and the TP battle was also quite disappointing
Others that aren't as good: King Dodongo, Morpheel, Moldarach